1G3W - JenaLib

Asymmetric Unit (Jmol Viewer)

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Title :   CD-CYS102SER DTXR

Authors :   E. Pohl, J. Goranson-Siekierke, R. K. Holmes, W. G. J. Hol

Date :   25 Oct 00 (Deposition) - 25 Oct 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym. Unit : A
Biol. Unit 1: A  (2x)

Keywords :   Dna Binding Protein, Iron Binding Protein, Iron Dependent Regulator, Gene Regulation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Pohl, J. Goranson-Siekierke, M. K. Choi, T. Roosild, R. K. Holmes, W. G. Hol
Structures Of Three Diphtheria Toxin Repressor (Dtxr) Variants With Decreased Repressor Activity.
Acta Crystallogr. , Sect. D V. 57 619 2001
PubMed-ID: 11320302 | Reference-DOI: 10.1107/S090744490100230X
(for further references see the PDB file header)

Molecule 1 - DIPHTHERIA TOXIN REPRESSOR
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Mutation	:	YES
	Organism Scientific	:	CORYNEBACTERIUM DIPHTHERIAE
	Organism Taxid	:	1717
	Synonym	:	DTXR

		1
Asymmetric Unit	:	A
Biological Unit 1 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 2)

No.	Name	Count	Type	Full Name
1	CD	1	Ligand/Ion	CADMIUM ION
2	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	CD	-1	Ligand/Ion	CADMIUM ION
2	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:79 , GLU A:83 , HIS A:98 , SO4 A:303 , HOH A:469	BINDING SITE FOR RESIDUE CD A 290
2	AC2	SOFTWARE	GLU A:17 , MET A:76 , HIS A:79 , ARG A:80 , GLU A:83 , HIS A:98 , CD A:290 , HOH A:436 , HOH A:452 , HOH A:469	BINDING SITE FOR RESIDUE SO4 A 303

(no "SS Bond" information available for 1G3W)

(no "Cis Peptide Bond" information available for 1G3W)

Asymmetric Unit (11, 11)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_DTXR_CORDI_001 *	R	47	H	DTXR_CORDI	---	---	A	R	47	H
02	UniProt	VAR_DTXR_CORDI_004 *	I	165	V	DTXR_CORDI	---	---	A	I	165	V
03	UniProt	VAR_DTXR_CORDI_005 *	V	174	A	DTXR_CORDI	---	---	A	V	174	A
04	UniProt	VAR_DTXR_CORDI_006 *	S	191	T	DTXR_CORDI	---	---	A	S	191	T
05	UniProt	VAR_DTXR_CORDI_008 *	H	201	R	DTXR_CORDI	---	---	A	H	201	R
06	UniProt	VAR_DTXR_CORDI_009 *	S	205	R	DTXR_CORDI	---	---	A	S	205	R
07	UniProt	VAR_DTXR_CORDI_010 *	I	214	L	DTXR_CORDI	---	---	A	L	214	L
08	UniProt	VAR_DTXR_CORDI_011 *	I	214	Y	DTXR_CORDI	---	---	A	L	214	Y
09	UniProt	VAR_DTXR_CORDI_012 *	A	218	T	DTXR_CORDI	---	---	A	A	218	T
10	UniProt	VAR_DTXR_CORDI_013 *	I	221	M	DTXR_CORDI	---	---	A	I	221	M
11	UniProt	VAR_DTXR_CORDI_014 *	I	221	T	DTXR_CORDI	---	---	A	I	221	T
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (11, 22)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_DTXR_CORDI_001 *	R	47	H	DTXR_CORDI	---	---	A	R	47	H
02	UniProt	VAR_DTXR_CORDI_004 *	I	165	V	DTXR_CORDI	---	---	A	I	165	V
03	UniProt	VAR_DTXR_CORDI_005 *	V	174	A	DTXR_CORDI	---	---	A	V	174	A
04	UniProt	VAR_DTXR_CORDI_006 *	S	191	T	DTXR_CORDI	---	---	A	S	191	T
05	UniProt	VAR_DTXR_CORDI_008 *	H	201	R	DTXR_CORDI	---	---	A	H	201	R
06	UniProt	VAR_DTXR_CORDI_009 *	S	205	R	DTXR_CORDI	---	---	A	S	205	R
07	UniProt	VAR_DTXR_CORDI_010 *	I	214	L	DTXR_CORDI	---	---	A	L	214	L
08	UniProt	VAR_DTXR_CORDI_011 *	I	214	Y	DTXR_CORDI	---	---	A	L	214	Y
09	UniProt	VAR_DTXR_CORDI_012 *	A	218	T	DTXR_CORDI	---	---	A	A	218	T
10	UniProt	VAR_DTXR_CORDI_013 *	I	221	M	DTXR_CORDI	---	---	A	I	221	M
11	UniProt	VAR_DTXR_CORDI_014 *	I	221	T	DTXR_CORDI	---	---	A	I	221	T
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_DTXR	PS50944	DtxR-type HTH domain profile.	DTXR_CORDI	4-65	1	A:4-65
1	HTH_DTXR	PS50944	DtxR-type HTH domain profile.	DTXR_CORDW	4-65	1	A:4-65

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_DTXR	PS50944	DtxR-type HTH domain profile.	DTXR_CORDI	4-65	2	A:4-65
1	HTH_DTXR	PS50944	DtxR-type HTH domain profile.	DTXR_CORDW	4-65	2	A:4-65

(no "Exon" information available for 1G3W)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:211
 aligned with DTXR_CORDI | P0DJL7 from UniProtKB/Swiss-Prot  Length:226

    Alignment length:221
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223 
           DTXR_CORDI     4 LVDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMTPTGRTLATAVMRKHRLAERLLTDIIGLDINKVHDEACRWEHVMSDEVERRLVKVLKDVSRSPFGNPIPGLDELGVGNSDAAVPGTRVIDAATSMPRKVRIVQINEIFQVETDQFTQLLDADIRVGSEVEIVDRDGHITLSHNGKDVELIDDLAHTIRIE 224
               SCOP domains d1g3wa1 A:4-64 Diphtheria toxin repressor (DtxR)             d1g3wa2 A:65-140 Diphtheria toxin repressor (DtxR)                                 d1g3wa3 A:148-224 Diphtheria toxin repressor (DtxR   )                        SCOP domains
               CATH domains 1g3wA01 A:4-74 'winged helix' repressor DNA binding domain             1g3wA02 A:75-140 Diphtheria Toxin Repressor, domain 2                    1g3wA03 A:148-224  [code=2.30.30.90, no name defin   ed]                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhh..eee.....eeehhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhh...hhhhhhhhhhhh.............hhhhhh.-------.....................hhhhh...hhhhhhhhh......eeeee.---..eee....eee.hhhhhhhhee. Sec.struct. author
             SAPs(SNPs) (1) -------------------------------------------H---------------------------------------------------------------------------------------------------------------------V--------A----------------T---------R---R--------L---T--M--- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Y------T--- SAPs(SNPs) (2)
                PROSITE (2) HTH_DTXR  PDB: A:4-65 UniProt: 4-65                           --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1g3w A   4 LVDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMTPTGRTLATAVMRKHRLAERLLTDIIGLDINKVHDEASRWEHVMSDEVERRLVKVLKDVSRSPFGNPIPGLDELGV-------PGTRVIDAATSMPRKVRIVQINEIFQVETDQFTQLLDADIRVGSEVEIVD---HITLSHNGKDVELLDDLAHTIRIE 224
                                    13        23        33        43        53        63        73        83        93       103       113       123       133      |  -    |  153       163       173       183       193   |   203       213       223 
                                                                                                                                                                  140     148                                              197 201

Chain A from PDB  Type:PROTEIN  Length:211
 aligned with DTXR_CORDW | H2I233 from UniProtKB/Swiss-Prot  Length:226

    Alignment length:221
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223 
           DTXR_CORDW     4 LVDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMTPTGRTLATAVMRKHRLAERLLTDIIGLDINKVHDEACRWEHVMSDEVERRLVKVLKDVSRSPFGNPIPGLDELGVGNSDAAAPGTRVIDAATSMPRKVRIVQINEIFQVETDQFTQLLDADIRVGSEVEIVDRDGHITLSHNGKDVELLDDLAHTIRIE 224
               SCOP domains d1g3wa1 A:4-64 Diphtheria toxin repressor (DtxR)             d1g3wa2 A:65-140 Diphtheria toxin repressor (DtxR)                                 d1g3wa3 A:148-224 Diphtheria toxin repressor (DtxR   )                        SCOP domains
               CATH domains 1g3wA01 A:4-74 'winged helix' repressor DNA binding domain             1g3wA02 A:75-140 Diphtheria Toxin Repressor, domain 2                    1g3wA03 A:148-224  [code=2.30.30.90, no name defin   ed]                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhh...hhhhhhhhhh.hhhhhhhhhhhhhhh..eee.....eeehhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhh...hhhhhhhhhhhh.............hhhhhh.-------.....................hhhhh...hhhhhhhhh......eeeee.---..eee....eee.hhhhhhhhee. Sec.struct. author
             SAPs(SNPs) (1) -------------------------------------------H---------------------------------------------------------------------------------------------------------------------V--------A----------------T---------R---R--------L---T--M--- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Y------T--- SAPs(SNPs) (2)
                    PROSITE HTH_DTXR  PDB: A:4-65 UniProt: 4-65                           --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1g3w A   4 LVDTTEMYLRTIYELEEEGVTPLRARIAERLEQSGPTVSQTVARMERDGLVVVASDRSLQMTPTGRTLATAVMRKHRLAERLLTDIIGLDINKVHDEASRWEHVMSDEVERRLVKVLKDVSRSPFGNPIPGLDELGV-------PGTRVIDAATSMPRKVRIVQINEIFQVETDQFTQLLDADIRVGSEVEIVD---HITLSHNGKDVELLDDLAHTIRIE 224
                                    13        23        33        43        53        63        73        83        93       103       113       123       133      |  -    |  153       163       173       183       193   |   203       213       223 
                                                                                                                                                                  140     148                                              197 201

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "Pfam Domain" information available for 1G3W)

Asymmetric Unit(hide GO term definitions)

Chain A (DTXR_CORDW | H2I233)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0046983	protein dimerization activity	The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
	GO:0003700	transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
	GO:0046914	transition metal ion binding	Interacting selectively and non-covalently with a transition metal ions; a transition metal is an element whose atom has an incomplete d-subshell of extranuclear electrons, or which gives rise to a cation or cations with an incomplete d-subshell. Transition metals often have more than one valency state. Biologically relevant transition metals include vanadium, manganese, iron, copper, cobalt, nickel, molybdenum and silver.
biological process
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain A (DTXR_CORDI | P0DJL7)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0046983	protein dimerization activity	The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
	GO:0003700	transcription factor activity, sequence-specific DNA binding	Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
	GO:0046914	transition metal ion binding	Interacting selectively and non-covalently with a transition metal ions; a transition metal is an element whose atom has an incomplete d-subshell of extranuclear electrons, or which gives rise to a cation or cations with an incomplete d-subshell. Transition metals often have more than one valency state. Biologically relevant transition metals include vanadium, manganese, iron, copper, cobalt, nickel, molybdenum and silver.
biological process
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
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Biological Unit
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	1g3w
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	DTXR_CORDW \| H2I233
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1fwz	DXTR E20A MUTANT
1g3s	DXTR C102S MUTANT IN P 31 2 1 SPACE GROUP
1g3t	DXTR C102S MUTANT IN P 32 2 1 SPACE GROUP
1g3y	DXTR R80A MUTANT

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (11, 11)

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Exons (0, 0)

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SCOP Domains (3, 3)

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Gene Ontology (7, 14)

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